In a large bowl, whisk together almond flour, salt, baking powder, and cinnamon. In another bowl, whisk together honey, oil, milk, vanilla, egg, and baking soda. Pour the wet ingredients into the dry and mix until just combined. Add the the grated apples and pecans and gently mix.
Scoop the batter into the prepared muffin pan, filling the muffin cup almost to the top. Mix together the sugar and cinnamon and sprinkle the tops, and bake for 15-18 minutes for standard muffins or 12-17 minutes for mini muffins, until muffins are browned and a toothpick comes out clean. Let cool on a wire rack for 5 minutes, then remove the muffins from the pan and continue to cool on the rack.